Pathogenomics and Evolutionary Epidemiology of Multi-Drug Resistant Clinical Klebsiella pneumoniae Isolated from Pretoria, South Africa

Abstract

Antibiotic-resistant Klebsiella pneumoniae is increasingly being implicated in invasive infections worldwide with high mortalities. forty-two multidrug resistant (MDR) K. pneumoniae isolates were collected over a 4-month period. Antimicrobial susceptibility was determined using Microscan. The evolutionary epidemiology, resistome, virulome and mobilome of the isolates were characterised using whole-genome sequencing and bioinformatics analysis. All isolates contained the bla ctX-M gene, whilst 41/42(97%) contained bla teM , 36/42(86%) contained bla oXA and 35/42(83%) harboured bla SHV genes. other resistance genes found included bla Len , aac(6′)-lb-cr, qnrA, qnrB, qnrS, oqxAB, aad, aph, dfr, sul1, sul2, fosA, and cat genes. fluoroquinolone and colistin resistance-conferring mutations in parc, gyrAB, pmrAB, phopQ and kpnEF were identified. The bla Len gene, rarely described worldwide, was identified in four isolates. The isolates comprised diverse sequence types, the most common being ST152 in 7/42(17%) isolates; clone-specific O and K capsule types were identified. Diverse virulence genes that were not clone-specific were identified in all but one isolate. IncF, IncH and IncI plasmid replicons and two novel integrons were present. the bla CTX-M-15 and bla TEM-1 genes were bracketed by Tn3 transposons, ISEc9, a resolvase and IS91 insertion sequence. There were 20 gene cassettes in 14 different cassette arrays, with the dfrA and aadA gene cassettes being the most frequent. phylogenetic analysis demonstrated that the isolates were evolutionarily associated with strains from both South Africa and abroad. These findings depict the rich resistome, mobilome and virulome repertoire in clinical K. pneumoniae strains, which are mainly transmitted by clonal, multiclonal and horizontal means in South Africa.Antibiotic resistance (ABR) is a global phenomenon widely described in the literature 1,2 , and is associated with treatment failure, as well as increased morbidity and mortality 3-5 . Dissemination of resistance in bacteria, particularly among Enterobacteriaceae, is mainly due to the exchange of ABR genes (ARGs) between and within species, mediated by mobile genetic elements (MGEs) harbouring ARGs 6-8 . MGEs include plasmids, transposons and integrons that are known to transmit ABR in both Gram-positive and Gram-negative bacteria, including cephalosporin-and carbapenem-resistant Enterobacteriaceae that have been classified as critical priority pathogens by the WHO 9 . Integrons that capture cassettes i.e., single gene fragments, usually insert into transposons, enabling their movement between bacteria. Of the eight integron classes described, class 1, 2 and 3 are associated with antimicrobial resistance although class 1 is more frequently described in the literature 6,10-12 .

Occurrence, identification, and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa

“…The presence of these key ESBL genes in clinical and environmental contexts have been previously described among Klebsiella spp. in South African and international isolates [89][90][91][92]. Since the isolates did not display full resistance to carbapenems and consequently did not harbour any of the carbapenemases genes, it was assumed that these could be kept as reserve drugs to treat infections caused by Klebsiella spp.…”

Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains

“…Acquisition of antimicrobial-inactivating enzymes and efflux pump systems are important in the development of multi-drug resistant (MDR) in Enterobacterales, including K. pneumoniae [9,10], with the resistance-nodulation-division (RND) family of efflux pumps being responsible for ejecting charged and amphiphilic antimicrobials such as aminoglycosides, β-lactams and fluoroquinolones [10,11]. The use of β-lactams over the years has resulted in widespread escalation of β-lactamases, including carbapenemase-producing K. pneumoniae [12,13], resulting in increased treatment failure, morbidity and mortality [14]. High-level resistance in K. pneumoniae isolates is typically mediated by the production of carbapenemases and/or porin loss with the production of either extended-spectrum β-lactamase (ESBL) or an AmpC [15].…”

“…In Africa and South Africa, K. pneumoniae clones that are commonly reported include ST101, ST152, ST39, ST1414, ST14, ST15 and ST307, with the global ST258 clone being relatively rare [13,19,20]. Of the several virulence factors found in K. pneumoniae, K1 and K2 capsular types have been found to proffer hypervirulence characteristics to this species.…”

“…MGEs such as plasmids, transposons, prophages and integrons play a major role in the acquisition and dissemination of ARGs in carbapenem-resistant strains [13,20,30,31]. Among these are large conjugative plasmids that have been associated with horizontal gene transfer (HGT) of carbapenemases between and within Gram-negative bacteria [8].…”

“…These plasmids have been reported in K. pneumoniae strains and are associated with multiple replicon groups such as IncF, A/C, L/M, N and X [30]. IncF replicon plasmids are the most predominant and are mainly reported to carry the bla KPC and bla NDM genes in the USA, Canada, Greece, South Africa and Taiwan [13,20,30,32]. The L/M plasmids in K. pneumoniae are more frequently reported in the Czech Republic and…”